5AMO | pdb_00005amo

Structure of a mouse Olfactomedin-1 disulfide-linked dimer of the Olfactomedin domain and part of the coiled coil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5AMO

Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Olfactomedin-1 Has a V-Shaped Disulfide-Linked Tetrameric Structure.

Pronker, M.F.Bos, T.G.A.A.Sharp, T.H.Thies-Weesie, D.M.Janssen, B.J.C.

(2015) J Biological Chem 290: 15092

  • DOI: https://doi.org/10.1074/jbc.M115.653485
  • Primary Citation Related Structures: 
    5AMO

  • PubMed Abstract: 

    Olfactomedin-1 (Olfm1; also known as noelin and pancortin) is a member of the olfactomedin domain-containing superfamily and a highly expressed neuronal glycoprotein important for nervous system development. It binds a number of secreted proteins and cell surface-bound receptors to induce cell signaling processes. Using a combined approach of x-ray crystallography, solution scattering, analytical ultracentrifugation, and electron microscopy we determined that full-length Olfm1 forms disulfide-linked tetramers with a distinctive V-shaped architecture. The base of the "V" is formed by two disulfide-linked dimeric N-terminal domains. Each of the two V legs consists of a parallel dimeric disulfide-linked coiled coil with a C-terminal β-propeller dimer at the tips. This agrees with our crystal structure of a C-terminal coiled-coil segment and β-propeller combination (Olfm1(coil-Olf)) that reveals a disulfide-linked dimeric arrangement with the β-propeller top faces in an outward exposed orientation. Similar to its family member myocilin, Olfm1 is stabilized by calcium. The dimer-of-dimers architecture suggests a role for Olfm1 in clustering receptors to regulate signaling and sheds light on the conformation of several other olfactomedin domain family members.


  • Organizational Affiliation
    • From the Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research and.

Macromolecule Content 

  • Total Structure Weight: 110.6 kDa 
  • Atom Count: 4,304 
  • Modeled Residue Count: 510 
  • Deposited Residue Count: 942 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NOELIN
A, B
471Mus musculusMutation(s): 1 
UniProt
Find proteins for O88998 (Mus musculus)
Explore O88998 
Go to UniProtKB:  O88998
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO88998
Glycosylation
Glycosylation Sites: 3Go to GlyGen: O88998-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.22α = 90
b = 43.94β = 114.17
c = 104.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-05-06
    Changes: Database references, Derived calculations
  • Version 1.2: 2015-07-01
    Changes: Database references
  • Version 1.3: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Structure summary